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JinmiaoChenLab / cytofkit

cytofkit: an integrated flow/mass cytometry data analysis pipeline
http://jinmiaochenlab.github.io/cytofkit/
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cytofkit does not generate new .fcs files #50

Open ctjiam opened 5 years ago

ctjiam commented 5 years ago

Hi,

I have encountered a problem when using cytofkit (via GUI) and would like to know if anyone else has encountered something similar. cytofkit is not outputting any .fcs files in the result directory and comes up with the error messages:

Error in if (nchar(shape_string[1]) <= 1) { : missing value where TRUE/FALSE needed In addition: Warning message: Removed 4357 rows containing missing values (geom_point).

I have noticed that if i set the clustering option to NULL these errors do not occur and new .fcs files are generated.

Also, if the input number of flow cytometry events (rows) is <14553, even with clustering set to Rphenograph (k=30), these errors do not occur and new .fcs files are generated.

I am running: R 3.5.1 cytofkit 1.11.3 flowCore 1.47.9 Windows 7 (64-bit) fcs/output directories on computer's SSD

Would anyone know what could be causing this issue? I would highly appreciate any help on this matter.

Kind regards

Chris

lconde-ucl commented 5 years ago

Hi Chris, I'm having the same issue, did you ever find out what the cause was? Lucia

lconde-ucl commented 5 years ago

FYI, the cause of the problem is described here: https://github.com/JinmiaoChenLab/cytofkit2/issues/14#issuecomment-539503309_

grhogg commented 4 years ago

I am struggling with the problem of not generating any .Rdata when I run large batches of FCS files (say 35) through the cytofkit2 GUI. Has there been any resolution for this problem? It works fine for me when I run smaller batches (say 10)